Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ARID1A

Cell type

Cell type Class
Breast
Cell type
MCF 10A
Primary Tissue
Breast
Tissue Diagnosis
Fibrocystic Disease

Attributes by original data submitter

Sample

source_name
human non-transformed breast epithelial cell
cell type
human non-transformed breast epithelial cell
cell line
MCF10A
chip antibody
ARID1A (CST, #12354)
genotype
ARID5A knockdown group

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with ARID1A antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (TruSeq® chip DNA LT Sample Prep Kit), including performing end repair, adenylating 3' ends, ligating adapters and enriching DNA Fragments. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
23868012
Reads aligned (%)
58.4
Duplicates removed (%)
12.9
Number of peaks
289 (qval < 1E-05)

hg19

Number of total reads
23868012
Reads aligned (%)
57.6
Duplicates removed (%)
13.4
Number of peaks
189 (qval < 1E-05)

Base call quality data from DBCLS SRA